Our (at least) amd64 & x86 stage3s are shipping a make.conf with a CPU_FLAGS_X86 which is either same as or worse than what profiles already set. This is causing problems like bug 544696. There is some discussion on bug 559280 but that is currently a portage bug, this one is for release team & stage3 issues. This is fixed in newer catalyst-3.0_rc1 but until that's what's producing our stage3's, this issue persists
*** This bug has been marked as a duplicate of bug 559280 ***